[Bioc-devel] RBGL 1.12 compile/install issue

[Li.Long at isb-sib.ch]

> Hello Li, hello list
>
......
>
> $(SHLIB): $(OBJECTS)
>         $(SHLIB_LINK) -o $@ $(OBJECTS) $(ALL_LIBS)
>
> and my etc/Makeconf:
> SHLIB_CFLAGS =
> SHLIB_CXXFLAGS =
> SHLIB_CXXLD = g++
> SHLIB_CXXLDFLAGS =
> SHLIB_EXT = .so
> SHLIB_FCLD = g77
> SHLIB_FCLDFLAGS = -shared
> SHLIB_FFLAGS =
> SHLIB_LD = gcc -std=gnu99
> SHLIB_LDFLAGS = -shared
> SHLIB_LIBADD =
> SHLIB_LINK = $(SHLIB_LD) $(SHLIB_LDFLAGS) $(LDFLAGS)
>

If this is really what's used, you SHOULD get

g++ -shared -o RBGL.so ....

You could try to modify the 1st line in .../R-2.5.0/bin/INSTALL to

#! /bin/sh -xv

to turn on the echos to see what happens when running
    .../R-2.5.0/bin/R CMD INSTALL .../RBGL

Just for your reference, here's what I see from my run:

......
++ sh /home/vital-it/lilong/R-src/R-2.5.0/bin/SHLIB -o RBGL.so bbc.cpp
cliques.cpp clusteringCoef.cpp hcs.cpp incrConnComp.cpp interfaces.cpp
layout.cpp mincut.cpp minST.cpp ordering.cpp shortestPath.cpp sna.cpp
transitive_closure.cpp wavefront.cpp
g++ -shared -L/usr/local/lib -o RBGL.so bbc.o cliques.o clusteringCoef.o
hcs.o incrConnComp.o interfaces.o layout.o mincut.o minST.o ordering.o
shortestPath.o sna.o transitive_closure.o wavefront.o
......

You can see that SHLIB is expanded to
     g++ -shared -L/usr/local/lib
correctly.

Let me know what I could help.

Li